Hi Micha,

I'm wondering what to do in order to create a custom error model. I would like to create a simulation for 100 base pair reads.

Here, 4.5.3 - Output Read Sequences it says

With the values '35' or '76', default error models are provided for the corresponding read lengths, otherwise the path to a custom error model file is expected.

But, here 4.5.4 - Error Models  it says

Since Version 1.0.3, the simulator model scaled to support read length not explicitly supported by the model. With this, you can for example use the 76bp error model and simulate error for 100bp reads

So do I need to generate a custom error model or not?

if yes, are there more detailed instructions about the procedure using GEM ? If not, would I just enter READ_LENGTH 100 and ERR_FILE 76 ?

thanks,

Maayan

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3 Comments

  1. Thasso Griebel

    Hi Maayan,

    no, you don't need to create a custom model. The default models will be scaled (so a little bit less accurate) but will work fine. I am still working on on update on the error model creation. The problem is that the current GEM format changed, so what we have in the Simulator currently only works with an old version of GEM. I will try to update the model creation and implement support for SAM/BAM files.

     

  2. mathieu

    Hi,

    I would also greatly appreciate the possibility to have a custom error model generated from bam/sam files. It would make this tools much more usefull.

    best,

    mathieu

  3. Micha Sammeth

    Corresponding request for improvement filed:

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